@danielblomma/cortex-mcp 2.0.16 → 2.0.19

package/scaffold/mcp/tests/workflow-synced-registry.test.mjs

@@ -8,6 +8,7 @@ import {
   loadSyncedWorkflows,
   syncedWorkflowsCachePath,
 } from "../dist/core/workflow/synced-registry.js";
+import { resolveWorkflowDefinition } from "../dist/core/workflow/resolution.js";
 import { runWorkflowStart } from "../dist/core/workflow/mcp-tools.js";
 import { SECURE_BUILD_WORKFLOW } from "../dist/core/workflow/default-workflows.js";
 
@@ -173,6 +174,61 @@ test("resolveWorkflow integration: synced cache adds new workflow_ids beyond def
     );
     assert.equal(result.state.workflow_id, "tiny");
     assert.equal(result.state.current_stage, "plan");
+    assert.equal(result.workflow_source, "synced");
+  } finally {
+    delete process.env.HOME;
+  }
+});
+
+test("resolveWorkflowDefinition: includes bundled fallback warning when synced cache lacks the requested id", () => {
+  const fakeHome = makeWorkspace();
+  process.env.HOME = fakeHome;
+  try {
+    const resolved = resolveWorkflowDefinition("secure-build", {
+      emitBundledFallbackWarning: true,
+    });
+    assert.equal(resolved.source, "bundled");
+    assert.equal(resolved.warnings.length, 1);
+    assert.match(resolved.warnings[0].message, /bundled registry/);
+  } finally {
+    delete process.env.HOME;
+  }
+});
+
+test("resolveWorkflowDefinition: can block bundled fallback when synced workflows are required", () => {
+  const fakeHome = makeWorkspace();
+  process.env.HOME = fakeHome;
+  try {
+    assert.throws(
+      () =>
+        resolveWorkflowDefinition("secure-build", {
+          bundledFallbackPolicy: "block",
+        }),
+      /requires a synced org workflow/,
+    );
+  } finally {
+    delete process.env.HOME;
+  }
+});
+
+test("resolveWorkflowDefinition: unknown workflow errors list bundled and synced ids", () => {
+  const fakeHome = makeWorkspace();
+  process.env.HOME = fakeHome;
+  try {
+    writeCache(path.join(fakeHome, ".cortex"), {
+      workflows: {
+        tiny: {
+          workflow_id: "tiny",
+          version: 1,
+          updated_at: "2026-05-06T12:00:00.000Z",
+          definition: TINY_WORKFLOW,
+        },
+      },
+    });
+    assert.throws(
+      () => resolveWorkflowDefinition("missing-workflow"),
+      /Available bundled: secure-build\. Available synced: tiny\./,
+    );
   } finally {
     delete process.env.HOME;
   }

package/scaffold/scripts/bootstrap.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 MCP_DIR="$REPO_ROOT/.context/mcp"
 TOTAL_STEPS=6
 STEP_INDEX=0
@@ -25,24 +26,24 @@ mkdir -p "$MCP_DIR/.npm-cache"
 step "Installing MCP dependencies"
 info "note: upstream RyuGraph dependencies may print deprecation warnings during install"
 NPM_CONFIG_CACHE="$MCP_DIR/.npm-cache" npm --prefix "$MCP_DIR" install --no-fund --no-update-notifier --loglevel=warn
-NPM_CONFIG_CACHE="$REPO_ROOT/scripts/parsers/.npm-cache" npm --prefix "$REPO_ROOT/scripts/parsers" install --no-fund --no-update-notifier --loglevel=warn
+NPM_CONFIG_CACHE="$REPO_ROOT/.context/scripts/parsers/.npm-cache" npm --prefix "$REPO_ROOT/.context/scripts/parsers" install --no-fund --no-update-notifier --loglevel=warn
 
-source "$REPO_ROOT/scripts/lib/enterprise-check.sh"
+source "$SCRIPT_DIR/lib/enterprise-check.sh"
 
 step "Indexing repository context"
-"$REPO_ROOT/scripts/ingest.sh"
+"$SCRIPT_DIR/ingest.sh"
 
 step "Generating semantic embeddings"
-if ! "$REPO_ROOT/scripts/embed.sh"; then
+if ! "$SCRIPT_DIR/embed.sh"; then
   info "warning: embedding generation failed; continuing with lexical search fallback"
 fi
 
 step "Loading RyuGraph"
-"$REPO_ROOT/scripts/load-ryu.sh"
+"$SCRIPT_DIR/load-ryu.sh"
 
 step "Reading context status"
-"$REPO_ROOT/scripts/status.sh"
+"$SCRIPT_DIR/status.sh"
 
 echo ""
 info "bootstrap complete"
-info "next: run ./scripts/context.sh update while coding"
+info "next: run cortex update while coding"

package/scaffold/scripts/context.sh

@@ -5,7 +5,7 @@ SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 print_help() {
   cat <<'EOF'
-Usage: ./scripts/context.sh <command> [options]
+Usage: cortex <command> [options]
 
 Commands:
   bootstrap                        Install deps + full ingest + graph load

package/scaffold/scripts/dashboard.mjs

@@ -6,7 +6,9 @@ import { execSync } from "node:child_process";
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
-const REPO_ROOT = path.resolve(__dirname, "..");
+const REPO_ROOT = process.env.CORTEX_PROJECT_ROOT
+  ? path.resolve(process.env.CORTEX_PROJECT_ROOT)
+  : path.resolve(__dirname, "..", "..");
 const CONTEXT_DIR = path.join(REPO_ROOT, ".context");
 const CACHE_DIR = path.join(CONTEXT_DIR, "cache");
 const CONFIG_PATH = path.join(CONTEXT_DIR, "config.yaml");

package/scaffold/scripts/dashboard.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 set -euo pipefail
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-REPO_ROOT="$(cd "$SCRIPT_DIR/.." && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 MANIFEST="$REPO_ROOT/.context/cache/manifest.json"
 
 if [[ ! -f "$MANIFEST" ]]; then

package/scaffold/scripts/doctor.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 CONTEXT_DIR="$REPO_ROOT/.context"
 MCP_DIR="$CONTEXT_DIR/mcp"
 

package/scaffold/scripts/embed.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 MCP_DIR="$REPO_ROOT/.context/mcp"
 
 if ! command -v npm >/dev/null 2>&1; then

package/scaffold/scripts/ingest.mjs

@@ -91,7 +91,9 @@ async function loadOptionalParsers() {
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
-const REPO_ROOT = path.resolve(__dirname, "..");
+const REPO_ROOT = process.env.CORTEX_PROJECT_ROOT
+  ? path.resolve(process.env.CORTEX_PROJECT_ROOT)
+  : path.resolve(__dirname, "..", "..");
 const CONTEXT_DIR = path.join(REPO_ROOT, ".context");
 const CACHE_DIR = path.join(CONTEXT_DIR, "cache");
 const DB_IMPORT_DIR = path.join(CONTEXT_DIR, "db", "import");

package/scaffold/scripts/ingest.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 CONTEXT_DIR="$REPO_ROOT/.context"
 
 printf "[ingest] repo: %s\n" "$REPO_ROOT"
@@ -17,4 +18,4 @@ if ! command -v node >/dev/null 2>&1; then
   exit 1
 fi
 
-node "$REPO_ROOT/scripts/ingest.mjs" "$@"
+node "$SCRIPT_DIR/ingest.mjs" "$@"

package/scaffold/scripts/install-git-hooks.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 HOOKS_DIR="$REPO_ROOT/.githooks"
 
 if [[ ! -d "$HOOKS_DIR" ]]; then

package/scaffold/scripts/load-kuzu.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 echo "[graph-load] warning: load-kuzu.sh is deprecated; using RyuGraph loader"
-"$REPO_ROOT/scripts/load-ryu.sh" "$@"
+"$SCRIPT_DIR/load-ryu.sh" "$@"

package/scaffold/scripts/load-ryu.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 MCP_DIR="$REPO_ROOT/.context/mcp"
 
 if [[ ! -f "$MCP_DIR/package.json" ]]; then

package/scaffold/scripts/memory-compile.mjs

@@ -2,7 +2,7 @@
 import fs from "node:fs";
 import path from "node:path";
 import { fileURLToPath } from "node:url";
-import { parseFrontmatter, parseStringList } from "../.context/mcp/dist/frontmatter.js";
+import { parseFrontmatter, parseStringList } from "../mcp/dist/frontmatter.js";
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
@@ -17,7 +17,7 @@ function normalizeForWsl(rawPath) {
 
 const REPO_ROOT = process.env.CORTEX_PROJECT_ROOT
   ? path.resolve(normalizeForWsl(process.env.CORTEX_PROJECT_ROOT))
-  : path.resolve(__dirname, "..");
+  : path.resolve(__dirname, "..", "..");
 const CONTEXT_DIR = path.join(REPO_ROOT, ".context");
 const MEMORY_DIR = path.join(CONTEXT_DIR, "memory");
 const RAW_DIR = path.join(MEMORY_DIR, "raw");

package/scaffold/scripts/memory-compile.sh

@@ -2,7 +2,8 @@
 # Keep in sync with scripts/memory-compile.sh
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 CONTEXT_DIR="$REPO_ROOT/.context"
 
 printf "[memory-compile] repo: %s\n" "$REPO_ROOT"
@@ -17,4 +18,4 @@ if ! command -v node >/dev/null 2>&1; then
   exit 1
 fi
 
-node "$REPO_ROOT/scripts/memory-compile.mjs" "$@"
+CORTEX_PROJECT_ROOT="$REPO_ROOT" node "$SCRIPT_DIR/memory-compile.mjs" "$@"

package/scaffold/scripts/memory-lint.mjs

@@ -2,7 +2,7 @@
 import fs from "node:fs";
 import path from "node:path";
 import { fileURLToPath } from "node:url";
-import { parseFrontmatter, parseStringList } from "../.context/mcp/dist/frontmatter.js";
+import { parseFrontmatter, parseStringList } from "../mcp/dist/frontmatter.js";
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
@@ -17,7 +17,7 @@ function normalizeForWsl(rawPath) {
 
 const REPO_ROOT = process.env.CORTEX_PROJECT_ROOT
   ? path.resolve(normalizeForWsl(process.env.CORTEX_PROJECT_ROOT))
-  : path.resolve(__dirname, "..");
+  : path.resolve(__dirname, "..", "..");
 const CONTEXT_DIR = path.join(REPO_ROOT, ".context");
 const MEMORY_DIR = path.join(CONTEXT_DIR, "memory");
 const COMPILED_DIR = path.join(MEMORY_DIR, "compiled");

package/scaffold/scripts/memory-lint.sh

@@ -2,7 +2,8 @@
 # Keep in sync with scripts/memory-lint.sh
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 CONTEXT_DIR="$REPO_ROOT/.context"
 
 printf "[memory-lint] repo: %s\n" "$REPO_ROOT"
@@ -17,4 +18,4 @@ if ! command -v node >/dev/null 2>&1; then
   exit 1
 fi
 
-node "$REPO_ROOT/scripts/memory-lint.mjs" "$@"
+CORTEX_PROJECT_ROOT="$REPO_ROOT" node "$SCRIPT_DIR/memory-lint.mjs" "$@"

package/scaffold/scripts/parsers/node_modules/.package-lock.json

@@ -9,7 +9,6 @@
       "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.16.0.tgz",
       "integrity": "sha512-UVJyE9MttOsBQIDKw1skb9nAwQuR5wuGD3+82K6JgJlm/Y+KI92oNsMNGZCYdDsVtRHSak0pcV5Dno5+4jh9sw==",
       "license": "MIT",
-      "peer": true,
       "bin": {
         "acorn": "bin/acorn"
       },

package/scaffold/scripts/parsers/package-lock.json

@@ -21,7 +21,6 @@
       "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.16.0.tgz",
       "integrity": "sha512-UVJyE9MttOsBQIDKw1skb9nAwQuR5wuGD3+82K6JgJlm/Y+KI92oNsMNGZCYdDsVtRHSak0pcV5Dno5+4jh9sw==",
       "license": "MIT",
-      "peer": true,
       "bin": {
         "acorn": "bin/acorn"
       },

package/scaffold/scripts/refresh.sh

@@ -1,9 +1,9 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 echo "[refresh] running ingestion"
-"$REPO_ROOT/scripts/ingest.sh" "$@"
+"$SCRIPT_DIR/ingest.sh" "$@"
 
 echo "[refresh] done"

package/scaffold/scripts/status.sh

@@ -1,14 +1,15 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 MANIFEST="$REPO_ROOT/.context/cache/manifest.json"
 GRAPH_MANIFEST="$REPO_ROOT/.context/cache/graph-manifest.json"
 EMBED_MANIFEST="$REPO_ROOT/.context/embeddings/manifest.json"
 
 if [[ ! -f "$MANIFEST" ]]; then
   echo "[status] No ingest manifest found."
-  echo "[status] Run: ./scripts/context.sh ingest"
+  echo "[status] Run: cortex ingest"
   exit 0
 fi
 
@@ -47,7 +48,7 @@ console.log(`[status] graph files=${c.files ?? 0} rules=${c.rules ?? 0} adrs=${c
 console.log(`[status] graph rels constrains=${c.constrains ?? 0} implements=${c.implements ?? 0} supersedes=${c.supersedes ?? 0}`);
 ' "$GRAPH_MANIFEST"
 else
-  echo "[status] graph manifest missing (run: ./scripts/context.sh graph-load)"
+  echo "[status] graph manifest missing (run: cortex graph-load)"
 fi
 
 if [[ -f "$EMBED_MANIFEST" ]]; then
@@ -68,13 +69,13 @@ if (embedded > 0 && output > 0 && failed === 0) {
 } else if (embedded > 0 && output > 0) {
   console.log(`[status] semantic_search=embedding+lexical-partial (failed=${failed})`);
 } else if (entities > 0) {
-  console.log("[status] semantic_search=lexical-only (run: ./scripts/context.sh embed)");
+  console.log("[status] semantic_search=lexical-only (run: cortex embed)");
 } else {
   console.log("[status] semantic_search=lexical-only (no indexed entities)");
 }
 ' "$EMBED_MANIFEST"
 else
-  echo "[status] embeddings manifest missing (run: ./scripts/context.sh embed)"
+  echo "[status] embeddings manifest missing (run: cortex embed)"
   echo "[status] semantic_search=lexical-only (embeddings manifest missing)"
 fi
 

package/scaffold/scripts/update-context.sh

@@ -1,18 +1,18 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 echo "[update] ingesting changed files"
-"$REPO_ROOT/scripts/ingest.sh" --changed
+"$SCRIPT_DIR/ingest.sh" --changed
 
 echo "[update] embedding changed entities"
-if ! "$REPO_ROOT/scripts/embed.sh" --changed; then
+if ! "$SCRIPT_DIR/embed.sh" --changed; then
   echo "[update] warning: embedding generation failed; continuing with lexical search fallback"
 fi
 
 echo "[update] rebuilding graph"
-"$REPO_ROOT/scripts/load-ryu.sh"
+"$SCRIPT_DIR/load-ryu.sh"
 
 echo "[update] status"
-"$REPO_ROOT/scripts/status.sh"
+"$SCRIPT_DIR/status.sh"

package/scaffold/scripts/watch.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
 WATCH_DIR="$REPO_ROOT/.context/watch"
 PID_FILE="$WATCH_DIR/watch.pid"
 STAMP_FILE="$WATCH_DIR/last-stamp.sha1"
@@ -21,7 +22,7 @@ EVENT_BACKEND=""
 
 print_usage() {
   cat <<'USAGE'
-Usage: ./scripts/watch.sh [start|stop|status|run|once] [--interval <sec>] [--debounce <sec>] [--mode <auto|event|poll>]
+Usage: cortex watch [start|stop|status|run|once] [--interval <sec>] [--debounce <sec>] [--mode <auto|event|poll>]
 
 Commands:
   start     Start background watch loop
@@ -149,8 +150,8 @@ status_digest() {
   # .context/ excludes the relocated .context/mcp/ tree as well.
   find "$REPO_ROOT" -type f \
     ! -path "$REPO_ROOT/.context/*" \
-    ! -path "$REPO_ROOT/scripts/parsers/node_modules/*" \
-    ! -path "$REPO_ROOT/scripts/parsers/.npm-cache/*" \
+    ! -path "$REPO_ROOT/.context/scripts/parsers/node_modules/*" \
+    ! -path "$REPO_ROOT/.context/scripts/parsers/.npm-cache/*" \
     -print \
     | LC_ALL=C sort \
     | shasum -a 1 \
@@ -162,7 +163,7 @@ run_update() {
   start_ts="$(date -u +"%Y-%m-%dT%H:%M:%SZ")"
   echo "[watch] update start at $start_ts"
 
-  if bash "$REPO_ROOT/scripts/context.sh" update; then
+  if bash "$SCRIPT_DIR/context.sh" update; then
     echo "[watch] update success"
     return 0
   fi
@@ -199,15 +200,13 @@ wait_for_change_event() {
     inotifywait)
       inotifywait -q -r \
         -e modify,create,delete,move \
-        --exclude '(^|/)\\.git(/|$)|(^|/)\\.context(/|$)|(^|/)scripts/parsers/(node_modules|\\.npm-cache)(/|$)' \
+        --exclude '(^|/)\\.git(/|$)|(^|/)\\.context(/|$)' \
         "$REPO_ROOT" >/dev/null 2>&1 || true
       ;;
     fswatch)
       fswatch -1 -r \
         --exclude '(^|/)\\.git(/|$)' \
         --exclude '(^|/)\\.context(/|$)' \
-        --exclude '(^|/)scripts/parsers/node_modules(/|$)' \
-        --exclude '(^|/)scripts/parsers/\\.npm-cache(/|$)' \
         "$REPO_ROOT" >/dev/null 2>&1 || true
       ;;
     *)